Just to clarify what Eleanor is saying:
It was pointed out earlier (by James Holton, if I remember correctly?)
that only the vibration in the direction parallel to the diffraction
vector matters. If the mean-squared vibration in that direction is
1A^2, then the B-factor will be about 80A^2 (8*Pi^2 to be precise).
However, people tend to think of mean-square displacements in 3D
space. If the vibration is isotropic, then there is equal vibration
in the two directions perpendicular to the diffraction vector (which
don't affect the falloff of the scattering from that atom), and the
overall mean-square displacement is 3 times the mean-square
displacement in any one direction. So if you're thinking in terms of
3D mean-square displacement, you have to divide by 3 to get the
displacement parallel to the diffraction vector. In that case, an
atom with an overall 3D mean-square displacement of 1A^2 has a B-
factor of about 26A^2 (8*Pi^2/3).
Regards,
Randy Read
On 11 Dec 2008, at 09:39, Eleanor Dodson wrote:
> A small molecule crystallography text would give you the
> formulation for an ideal case.
> A rough guide is that a B factor of 80 is equivalent to a mean
> vibration about the coordinate of 1A
>
> But for proteins the B factor becomes the collection bin for all
> sorts of other errors - unrecognised multiple conformations, , and
> the restraints used make it harder to interpret.
>
> Eleanor
>
> Jacob Keller wrote:
>> Hello Crystallographers,
>>
>> does anybody have a good reference dealing with interpretations of
>> what B-factors (anisotropic or otherwise) really signify? In other
>> words, a systematic addressing of all of the possible underlying
>> molecular/crystal/data-collection phenomena which the B-factor
>> mathematically models?
>>
>> Thanks in advance,
>>
>> Jacob
>>
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> Dallos Laboratory
>> F. Searle 1-240
>> 2240 Campus Drive
>> Evanston IL 60208
>> lab: 847.491.2438
>> cel: 773.608.9185
>> email: [log in to unmask]
>> *******************************************
>>
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-
structmed.cimr.cam.ac.uk
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